maigesPreRaw-class {maigesPack} | R Documentation

## maigesPreRaw class, store pre raw microarray datasets

### Description

This class describes objects to handle data values and information about genes and samples used in the data. Here, it is possible to put any field from data tables that you want.

### Details

This class of objects is intended to define an intermediate step between the external world (data tables, gene groups, gene networks, etc) and real raw objects given by the class `maigesRaw`. In this intermediate step the user can do any type of exploratory analysis and set bad spots (at slot `BadSpots`), or to do any type of calculation they judge important in the fields of `Data` slot.

This class of objects is created by a call from `loadData`. The functions `addGeneGrps` and `addPaths` may also be used to add information for gene groups and gene networks. After the exploratory analysis it must be converted in an object of class `maigesRaw` using the function `createMaigesRaw`.

If you have the package Rgraphviz installed and working it is possible to display the graphs stored in the slot `Paths` using the command `plot`.

### Slots

`Data`:

  contains a list with matrices. Each matrix has `nrow` = number of spots and `ncol` = number of data tables (or chips) with the numerical values of each data field specified by the user in the configuration file used as parameter for `loadData` function.

`GeneGrps`:

  a list containing character vectors. These vectors specify genes from the gene groups that must be studied. Each vector is used as a gene group. The names of the groups are catch from the names of the vectors from the list, that is catch from file names.

`Paths`:

  list containing `graphNEL` objects specifying gene regulatory networks (or pathways). As in the previous slot, the names are catch from file names and stored as names of the elements from the list.

`Layout`:

  a list containing the number of rows (`gridR`) and columns (`gridC`) of grids, the number of rows (`spotR`) and columns (`spotC`) of spots inside each grid and the total number of spots.

`Glabels`:

  data frame giving the gene labels. These labels are generally used during the data analysis.

`Slabels`:

  data frame giving the sample labels. These labels are generally used during the data analysis.

`BadSpots`:

  logical vector specifying spots that was judged as bad ones. By default this slot is created as a vector of FALSEs with same length as number of spots.

`Notes`:

  char string that receives any comment about the dataset. The dataset description is stored in this slot.

`Date`:

  char string giving the date and hour that the object was created.

`V.info`:

  list containg three characters. The first one is a string containing the R version used when the object was created. The second is a char vector with base packages and the last one is another char vector with additional packages and version numbers.

### Methods

print

  `signature(x = 'maigesPreRaw')`: print method for `maigesPreRaw` class.

show

  `signature(x = 'maigesPreRaw')`: show method for `maigesPreRaw` class.

summary

  `signature(x = 'maigesPreRaw')`: summary method for `maigesPreRaw` class.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### See Also

`loadData`, `addGeneGrps`, `addPaths`, `createMaigesRaw`.

[Package maigesPack version 1.52.0 Index]